# US 11,441,196 B2 · Ribosomal ribonucleic acid hybridization for organism identification

> Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt

- Number: US 11,441,196 B2
- Document ID: US11441196B2
- Status: Granted
- Kind: B2
- Application number: 14/775,296
- Filed: 2014-03-14
- Published: 2016-02-04
- Granted: 2022-09-13
- Earliest claimed: 2013-03-15
- Assignees: The Broad Institute, Inc.; The General Hospital Corporation
- Applicants: The Broad Institute, Inc.; The General Hospital Corporation
- Inventors: Roby Bhattacharyya; Deborah Hung; Jonathan Livny
- Web page: https://patentgrep.com/patent/US11441196B2

## CPC

- C12Q 1/689: for bacteria
- C12Q 2600/112: Disease subtyping, staging or classification
- C12Q 2600/158: Expression markers
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES

## Abstract

The present disclosure relates to method of distinguishing between two or more species of one or more organisms in a sample, by contacting a biological sample comprising ribosomal ribonucleic acid (rRNA) with a set of antisense probes, wherein the set of probes contains at least one detectable probe that is specific for a target rRNA sequence of each species to be tested, and wherein the individual probes specific for each species comprises less than about 85% sequence identity; and, detecting hybridization between one or more of the probes and the rRNA, thereby distinguishing between two or more species in a sample.

## Claims

### Claim 1

A method of detecting bacterial rRNA sequences in a sample, comprising:
contacting a sample with a set of probes, the set of probes comprising a plurality of different probes that hybridize to two or more different 5S target rRNA sequences, wherein each probe shares less than 80% identity with the other probes in the probe set and each probe is between 42 and 160 nucleotides in length,
hybridizing the set of probes to the target 5S rRNA sequences in the sample, and
detecting the target 5S rRNA sequences in the sample.

### Claim 2 (depends on 1)

The method of claim 1, wherein the probe set comprises one or more probes specific to one or more target rRNA sequences from two or more of Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, Acinetobacter baumannii, Candida albicans, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Proteus mirabilis, Streptococcus agalactiae, and Stenotrophomonas maltophilia.

### Claim 3 (depends on 1)

The method of claim 1, wherein the probe set comprises one or more probes specific to one or more target rRNA sequences for each of Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, Acinetobacter baumannii, Candida albicans, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Proteus mirabilis, Streptococcus agalactiae, and Stenotrophomonas maltophilia.

### Claim 4 (depends on 1)

The method of claim 1, wherein the probe set comprises one or more probes specific to each of E. coli, K pneumoniae, P. aeruginosa, and S. aureus.

### Claim 5 (depends on 1)

The method of claim 1, wherein the probe set is attached to a solid surface.

### Claim 6 (depends on 5)

The method of claim 5, wherein the probe set comprises probe pairs that bind to adjacent regions of a same target rRNA sequence.

### Claim 7 (depends on 6)

The method of claim 6, wherein a first probe of each probe pair comprises a detectable label and a second probe of each probe pairs comprises a capture moiety.

### Claim 8 (depends on 7)

The method of claim 7, wherein the detectable label is radiolabeled, fluorescently labeled, biotin-labeled, enzymatically-labeled, or chemically-labeled.

### Claim 9 (depends on 7)

The method of claim 7, wherein the capture moiety is biotin.

### Claim 10 (depends on 7)

The method of claim 7, wherein the first or second probe is bound to a solid surface.